The taxonomic position of a novel bacterial strain, YC5194T, with antimicrobial activity, isolated from the rhizosphere of pepper in Jinju, South Korea, was studied using a polyphasic approach. Cells of the strain were Gram-negative, rod-shaped, facultative anaerobes. It grew at a temperature of 15–37 °C (optimum 28 °C). Growth of the strain occurred between pH 5.5 and 8.5, with an optimum of pH 7.0–7.5. The strain inhibited mycelial growth of Pythium ultimum, Colletotrichum gloeosporioides, Fusarium oxysporum, Botrytis cinerea, Rhizoctonia solani and Botryosphaeria dothidea and growth of Bacillus subtilis. The G+C content of the total DNA was 65.4 mol%. The 16S rRNA gene sequence of the strain was most closely related to species of the genus Lysobacter (<94.0 to >99.0 % sequence similarity). Chemotaxonomic data (major quinone, Q-8; major polar lipids, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidyl-N-methylethanolamine; major fatty acids, iso-C15 : 0, summed feature 3, C16 : 0, iso-C17 : 1ω9c and C18 : 1ω7c) supported the affiliation of strain YC5194T to the genus Lysobacter. Phylogenetic analysis based on 16S rRNA gene sequences, DNA–DNA hybridization data and biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiation of strain YC5194T from species of Lysobacter with validly published names. Strain YC5194T therefore represents a novel species, for which the name Lysobacter capsici sp. nov. is proposed. The type strain is YC5194T (=KCTC 22007T =DSM 19286T).
Ahmed, K., Chohnan, S., Ohashi, H., Hirata, T., Masaki, T. & Sakiyama, F.(2003). Purification, bacteriolytic activity, and specificity of β-lytic protease from Lysobacter sp. IB-9374. J Biosci Bioeng95, 27–34.[CrossRef][Google Scholar]
Atlas, R. M.(1993).Handbook of Microbiological Media. Edited by L. C. Parks. Boca Raton, FL: CRC Press.
Ausubel, F. W., Brent, R., Kingston, R. E., Moore, D. D., Seidman, J. G., Smith, J. A. & Struhl, K.(1995).Current Protocols in Molecular Biology. New York: Wiley.
Cappuccino, J. G. & Sherman, N.(2002).Microbiology: a Laboratory Manual, 6th edn. Menlo Park, CA: Benjamin/Cummings.
Chohnan, S., Nonaka, J., Teramoto, K., Taniguchi, K., Kameda, Y., Tamura, H., Kurusu, Y., Norioka, S., Masaki, T. & Sakiyama, F.(2002).Lysobacter strain with high lysyl endopeptidase production. FEMS Microbiol Lett213, 13–20.[CrossRef][Google Scholar]
Christensen, P. & Cook, F. D.(1978).Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol28, 367–393.[CrossRef][Google Scholar]
Chung, Y. R., Sung, K. C., Mo, H. K., Son, D. Y., Nam, J. S., Chun, J. & Bae, K. S.(1999).Kitasatospora cheerisanensis sp. nov., a new species of the genus Kitasatospora that produces an antifungal agent. Int J Syst Bacteriol49, 753–758.[CrossRef][Google Scholar]
Chung, Y. R., Kim, C. H., Hwang, I. & Chun, J.(2000).Paenibacillus koreensis sp. nov., a new species that produces an iturin-like antifungal compound. Int J Syst Evol Microbiol50, 1495–1500.[CrossRef][Google Scholar]
Costilow, R. N.(1981). Biophysical factors in growth. Manual of Methods for General Bacteriology, pp. 66–78. Edited by P. Gerhardt, R. G. E. Murray, R. N. Costilow, E. W. Nester, W. A. Wood, N. R. Krieg & G. B. Phillips. Washington, DC: American Society for Microbiology.
Felsenstein, J.(1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution39, 783–791.[CrossRef][Google Scholar]
Fitch, W. M.(1971). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool20, 406–416.[CrossRef][Google Scholar]
Folman, L. B., De Klein, M. J. E. M., Postma, J. & van Veen, J. A.(2004). Production of antifungal compounds by Lysobacter enzymogenes isolate 3.1T8 under different conditions in relation to its efficacy as a biocontrol agent of Pythium aphanidermatum in cucumber. Biol Control31, 145–154.[CrossRef][Google Scholar]
Fox, G. E., Wisotzkey, J. D. & Jurtshuk, P., Jr(1992). How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol42, 166–170.[CrossRef][Google Scholar]
Hall, T. A.(1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser41, 95–98.
[Google Scholar]
Hashizume, H., Igarashi, M., Hattori, S., Hori, M., Hamada, M. & Takeuchi, T.(2001). Tripropeptins, novel antimicrobial agents produced by Lysobacter sp. J Antibiot (Tokyo)54, 1054–1059.[CrossRef][Google Scholar]
Hashizume, H., Hattor, S., Igarashi, M. & Akamatsu, Y.(2004). Tripropeptin E, a new tripropeptin group antibiotic produced by Lysobacter sp. BMK333-48F3. J Antibiot (Tokyo)57, 394–399.[CrossRef][Google Scholar]
Islam, M. T., Hashidoko, Y., Deora, A., Ito, T. & Tahara, S.(2005). Suppression of damping-off disease in host plants by the rhizoplane bacterium Lysobacter sp. strain SB-K88 is linked to plant colonization and antibiosis against soilborne Peronosporomycetes. Appl Environ Microbiol71, 3786–3796.[CrossRef][Google Scholar]
Kato, A., Nakaya, S., Kokubo, N., Aiba, Y., Ohashi, Y. & Hirata, H.(1998). A new anti-MRSA antibiotic complex, WAP-8294A. J Antibiot (Tokyo)51, 929–935.[CrossRef][Google Scholar]
Khan, A. A., Wang, R. F., Cao, W. W., Franklin, W. & Cerniglia, C. E.(1996). Reclassification of a polycyclic aromatic hydrocarbon-metabolizing bacterium, Beijerinckia sp. strain B1, as Sphingomonas yanoikuyae by fatty acid analysis, protein pattern analysis, DNA-DNA hybridization, and 16S ribosomal DNA sequencing. Int J Syst Bacteriol46, 466–469.[CrossRef][Google Scholar]
Kilic-Ekici, O. & Yuen, G. Y.(2003). Induced resistance as a mechanism of biological control by Lysobacter enzymogenes strain C3. Biol Control93, 1103–1110.
[Google Scholar]
Kimura, M.(1983).The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
Kumar, S., Tamura, K. & Nei, M.(2004).mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform5, 150–163.[CrossRef][Google Scholar]
Lane, D. J.(1991). 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by E. Stackebrandt & M. Goodfellow. Chichester: Wiley.
Lechevalier, M. P., De Bièvre, C. & Lechevalier, H. A.(1977). Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol5, 249–260.[CrossRef][Google Scholar]
Lee, J. W., Im, W.-T., Kim, M. K. & Yang, D.-C.(2006).Lysobacter koreensis sp. nov., isolated from a ginseng field. Int J Syst Evol Microbiol56, 231–235.[CrossRef][Google Scholar]
Lim, J. M., Jeon, C. O., Park, D. J., Kim, H. R., Yoon, B. J. & Kim, C. J.(2005).Pontibacillus marinus sp. nov., a moderately halophilic bacterium from a solar saltern, and emended description of the genus Pontibacillus. Int J Syst Evol Microbiol55, 1027–1031.[CrossRef][Google Scholar]
Mesbah, M., Premachandran, U. & Whitman, W. B.(1989). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol39, 159–167.[CrossRef][Google Scholar]
Nakayama, T., Homma, Y., Hashidoko, Y., Mizutani, J. & Tahara, S.(1999). Possible role of xanthobaccins produced by Stenotrophomonas sp. strain SB-K88 in suppression of sugar beet damping-off disease. Appl Environ Microbiol65, 4334–4339.
[Google Scholar]
Ryazanova, L. P., Stepnaya, O. A., Suzina, N. E. & Kulaev, I. S.(2005). Antifungal action of the lytic enzyme complex from Lysobacter sp. XL1. Process Biochem40, 557–564.[CrossRef][Google Scholar]
Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol4, 406–425.
[Google Scholar]
Sambrook, J. & Russell, D. W.(2001).Molecular Cloning: a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
Stackebrandt, E. & Goebel, B. M.(1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol44, 846–849.[CrossRef][Google Scholar]
Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A. D., Kämpfer, P., Maiden, M. C. J., Nesme, X., Rosselló-Mora, R., Swings, J. & other authors(2002). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol52, 1043–1047.[CrossRef][Google Scholar]
Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G.(1997). The clustal_x Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res25, 4876–4882.[CrossRef][Google Scholar]
Tindall, B. J.(1990). Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett66, 199–202.[CrossRef][Google Scholar]
Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & other authors(1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol37, 463–464.[CrossRef][Google Scholar]
Weon, H.-Y., Kim, B.-Y., Baek, Y.-K., Yoo, S.-H., Kwon, S.-W., Stackebrandt, E. & Go, S.-J.(2006). Two novel species, Lysobacter daejeonensis sp. nov. and Lysobacter yangpyeongensis sp. nov., isolated from Korean greenhouse soils. Int J Syst Evol Microbiol56, 947–951.[CrossRef][Google Scholar]
Yassin, A. F., Chen, W. M., Hupfer, H., Siering, C., Kroppenstedt, R. M., Arun, A. B., Lai, W. A., Shen, F. T., Rekha, P. D. & Young, C. C.(2007).Lysobacter defluvii sp. nov., isolated from municipal solid waste. Int J Syst Evol Microbiol57, 1131–1136.[CrossRef][Google Scholar]
Supplementary Fig. S1. Transmission electron micrographs
of cells of
Lysobacter capsici sp. nov. YC5194
Tin a 3 day-old culture cultivated on 0.1 %
TSA.